SNP probability score: The Bayesian posterior probability that a column of an alignment represents a polymorphic site, as opposed to a monomorphic site (A, C, G, or T). Calculated by the PolyBayes software.

Phred

Quality value of the base, calculated by the Phred software. Phred evaluates the trace surrounding each called base using four or five quality value parameters to quantify the trace quality. The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ), where P_e is the probability that the base call is an error. A quality value of, e.g., 30 means that the probability for the base call being an error is 10E-3 (0,001). (For more details see the Phred documentation.) The higher the PHRED value, the better is the trace quality, and the higher is the probability that the detected allele is true.

PLP (primer, seq., length)

PCR product length polymorphism assay for SNP genotyping. '1' if PLP assay has been verified, otherwise '0'. Created for >6nt long InDels, utilizing size differences between PCR products of the allelic variants. The genotype can be determined by separating PCR products on standard agarose gels. Typically, primers were designed so that PCR fragments are 130-230bp long for 7-20nt InDels, and 200-500bp for larger InDels. Primer sequences are indicated, if existing. Approximate PCR product lengths (bp) are also indicated.

Pos.1 / 2

Start and end of a SNP marker. Coordinates refer to Releases 3, 4, or 5, according to the user-specified selection.

Restriction fragment length polymorphism assay for SNP genotyping. '1' if RFLP assay has been predicted, otherwise '0'. If an RFLP site is predicted, a list of commercially available enzymes which cut differentially is specified.

SNP

Single nucleotide polymorphism. A (mostly) biallelic marker that can be used to distinguish two homologous chromosome regions of different origins. By definition, a SNP defines two alternative nucleotides that can occur at a specific site. The FLYSNP project uses an extended definition of SNPs which includes >1nt long polymorphisms and InDels. SNPs are specified by unique identifiers.

SNP marker

Set of closely linked SNPs, typically within an interval of ca. 1kb. A SNP marker may contain several SNPs. SNP markers are specified by unique identifiers.

SNP marker (old)

Names used in the first version of FLYSNPdb. The first 1-2 letters of the SNP marker name reflect the chromosome arm where the SNP marker is located.

SNP no. (old)

Names used in the first version of FLYSNPdb. The first 1-2 letters of the SNP marker name reflect the chromosome arm where the SNP marker is located.

SNP sites

Genomic site where a SNP was detected.

Stock count (max.)

Number of stocks from which genotype data is available. For SNP markers, the maximum stock count is specified.

Select chromosome arm, Release (for coordinates), and molecular or cytological region. The latter two options are mutually exclusive.
Following options are possible: "position 1 - position 2" -> region between these two positions; "position 1 + region length (nt)" -> region between pos.1 and pos.1+region length (the latter option currently only available for 'molecular').
Examples: "100000 - 500000"; "100000 + 400000"; "21B - 21D".
For selecting SNPs from whole chromosome arms, leave the 'Location' field blank.
If you would like to download the search result as FlyBase GBrowse track file, please select the most recent genome version, Release 5.

Select Stocks

Up to five stocks were genotyped at each SNP site. Only the SNP(marker)s which are differential between Stock1 and Stock2 are listed.
If alleles of all stocks should be listed, please select "all" for Stock1 and/or Stock2.
Summarized information about stocks used for SNP map creation:

The 'SNP marker' table shows general information on the marker region, whereas the 'SNP sites' table contains more detailed data on each SNP. Only one type of view is selectable for each search.
Data concerning quality scores, genotyping assays, coding information (according Rel5.10) or old IDs are optionally available. One or multiple options can be selected.

Submit Search or Browse all

After selection of the above described options press 'Submit'.
Alternatively, the 'Browse all' button can be selected, which shows all SNP markers or SNPs. The 'View' options and the 'Release' choice are also valid for 'Browse all'.

Query Result

The query result can be downloaded as text file (see menu after pressing 'Download').
The 'Go to GBrowse' link leads to the FlyBase genome browser page for showing a graphical representation of the selected genomic region.

Create Sub-selection

Sub-selections within the query result can be made by either clicking on the checkboxes at the left side of each row, or by entering search terms in the empty boxes (fields) below each column.
Multiple search criteria are possible (- resulting data will meet all criteria). Use '*' or '%' as wild card (in string searches, e.g. '*a*'), and '' in queries for lower or higher numbers (e.g. '>10000').
After pressing 'Submit', a new query result page will open.
It is thus possible to specifically select Indels by either entering '*-' into the 'Variant' field (SNP sites view), or by writing '>0' in the 'Indel length' field.

Download Query Result

Search result tables can be downloaded as text files with either tabulators ('tab-separated'), commas ('comma-separated') or semicolons ('semi-colon-separated') as separators.
It is also possible to download a FlyBase GBrowse track file containing the selected SNP marker or SNP site locations, which can be uploaded into GBrowse for graphical display.
Please note that the genome browser shows the most recent assembly version, Release 5.